Module TSS2: Using Sequence Alignment to Identify a TSS

This module illustrates how pairwise (blastn) and multiple sequence alignments can be used in conjunction with RNA-Seq data and the Short Match functionality of the UCSC Genome Browser to facilitate the TSS annotation of the Antp gene in D. eugracilis.

Module TSS3: CAGE, RAMPAGE, and RNA Pol II X-ChIP-Seq

This module uses the placement of the Initiator (Inr) motif, TSS annotations produced by the Celniker group at modENCODE, and experimental data such as CAGE, RAMPAGE, and RNA Polymerase II X-ChIP-Seq data to characterize the promoter for the Antp gene in D. melanogaster.

Searching for Transcription Start Sites in Drosophila

This PowerPoint presentation describes the recommended annotation strategy for identifying transcription start sites in Drosophila. The presentation provides an overview of the promoter architecture in D. melanogaster and describes the types of evidence that can be used to support the transcription start sites annotations.

TSS Annotation Workflow

This workflow provides an overview of the key steps and recommended search parameters for the annotation of transcription start sites.

Faculty Resources

  • All of the modules listed above are available with answer keys in a single package (automatic download) that uses members’ individual login credentials for the Project Management System.
  • A new version of the TSS Quiz is currently being beta tested. See Assessment Tools for more details.

About

The Transcription Start Sites (TSS) modules were developed by Margaret Laakso, Jamie Siders, and Michael Foulk. We would like to thank additional members of the GEP who helped to review and revise these modules.